\HeaderA{RGList\_CALIB-class}{Red, Green Intensity List - Class}{RGList.Rul.CALIB.Rdash.class}
\aliasA{coerce,RGList\_CALIB,exprSet2-method}{RGList\_CALIB-class}{coerce,RGList.Rul.CALIB,exprSet2.Rdash.method}
\aliasA{show,RGList\_CALIB-method}{RGList\_CALIB-class}{show,RGList.Rul.CALIB.Rdash.method}
\keyword{classes}{RGList\_CALIB-class}
\begin{Description}\relax
A simple list-based class for storing red and green channel foreground and 
background intensities for a batch of spotted microarrays. It is a extension of 
the RGList in the LIMMA package.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("RGList\_CALIB", RG)}, where RG is a list.
In the CALIB package, RGList\_CALIB objects are normally generated by
\code{read.rg}.
\end{Section}
\begin{Section}{List Components}
objects should contain the following list components:
\describe{ 
\item[\code{R}:] numeric matrix containing the red(Cy5) foreground intensities.
Rows correspond to spots and columns to arrays.

\item[\code{G}:] numeric matrix containing the green(Cy3) foreground intensities.

\item[\code{Rb}:] numeric matrix containing the red(Cy5) background intensities.

\item[\code{Gb}:] numeric matrix containing the green(Cy3) background intensities.

\item[\code{RArea}:] numeric matrix containing the red(Cy5) spot areas.

\item[\code{GArea}:] numeric matrix containing the green(Cy3) spot areas.
}

Optional components include:
\describe{
\item[\code{weights}:] numeric matrix containing relative spot quality weights.
Should be non-negative.

\item[\code{printer}:] list containing information on the process used to print
the spots on the arrays. See \code{\LinkA{read.rg}{read.rg}}.

\item[\code{genes}:] data.frame containing information on the genes spotted on
the arrays. Should include a character column Name containing names for the
genes or controls.

\item[\code{targets}:] data.frame containing information on the target RNA samples.
Should include factor or character columns Cy3 and Cy5 specifying which RNA was
hybridized to each array.

\item[\code{other}:] list containing numeric matrices of other spot-specific information.
}
All of the matrices should have the same dimensions. The row dimension of targets
should match the column dimension of the matrices.
\end{Section}
\begin{Section}{Extends}
Class \code{"list"}, from data part.
Class \code{"LargeDataObject"}, directly.
Class \code{"vector"}, by class \code{"list"}.
\end{Section}
\begin{Section}{Methods}
This class inherits directly from class List so any operation appropriate for lists will
work on objects of this class. In addition, RGList\_CALIB objects can be \code{\LinkA{subsetted}{subsetted}},
\code{\LinkA{combined}{combined}} and \code{\LinkA{merged}{merged}}. RGList\_CALIB objects
will return dimensions and hence functions such as \code{\LinkA{dim}{dim}},
\code{\LinkA{dimnames}{dimnames}}, \code{\LinkA{nrow}{nrow}} and
\code{\LinkA{ncol}{ncol}} are defined. RGList\_CALIB also inherit a \code{\LinkA{show}{show}}
method from the virtual class \code{\LinkA{LagerDataObject}{LagerDataObject}},
which means that RGList\_CALIB objects will print in a compact way.

In the CALIB package, RGList\_CALIB objects are mainly for storing microarray data and they are
used to pass microarray data into functions such as \code{\LinkA{estimateParameter}{estimateParameter}}
or \code{\LinkA{normalizeData}{normalizeData}}.
\end{Section}
\begin{Author}\relax
Hui Zhao
\end{Author}
\begin{References}\relax
\code{RGList} in the limma package
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{RGList}{RGList}} and \code{\LinkA{LargeDataObject}{LargeDataObject}} in limma packge.
\end{SeeAlso}

